Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression

Hiroaki Okae, Hitoshi Hiura, Yuichiro Nishida, Ryo Funayama, Satoshi Tanaka, Hatsune Chiba, Nobuo Yaegashi, Keiko Nakayama, Hiroyuki Sasaki, Takahiro Arima

    Research output: Contribution to journalArticle

    62 Citations (Scopus)

    Abstract

    Within the vertebrate groups, only mammals are subject to a specialized epigenetic process termed genomic imprinting in which genes are preferentially expressed from one parental allele. Imprinted expression has been reported for >100 mouse genes and, for approximately one-quarter of these genes, the imprinted expression is specific to the placenta (or extraembryonic tissues). This seemingly placenta-specific imprinted expression has garnered much attention, as has the apparent lack of conserved imprinting between the human and mouse placenta. In this study, we used a novel approach to re-investigate the placenta-specific expression using embryo transfer and trophoblast stem cells. We analyzed 20 genes previously reported to show maternal allele-specific expression in the placenta, and only 8 genes were confirmed to be imprinted. Other genes were likely to be falsely identified as imprinted due to their relatively high expression in contaminating maternal cells. Next, we performed a genome-wide transcriptome assay and identified 133 and 955 candidate imprinted genes with paternal allele- and maternal allele-specific expression. Of those we analyzed in detail, 1/6 (Gab1) of the candidates for paternal allele-specific expression and only 1/269 (Ano1) candidates for maternal allele-specific expression were authentically imprinted genes. Imprinting of Ano1 and Gab1 was specific to the placenta and neither gene displayed allele-specific promoter DNA methylation. Imprinting of ANO1, but not GAB1, was conserved in the human placenta. Our findings impose a considerable revision of the current views of placental imprinting.

    Original languageEnglish
    Article numberddr488
    Pages (from-to)548-558
    Number of pages11
    JournalHuman Molecular Genetics
    Volume21
    Issue number3
    DOIs
    Publication statusPublished - Feb 1 2012

    Fingerprint

    RNA Sequence Analysis
    Placenta
    Alleles
    Genes
    Mothers
    Genetic Epigenesis
    Genomic Imprinting
    Embryo Transfer
    Trophoblasts
    DNA Methylation
    Transcriptome
    Vertebrates
    Mammals
    Stem Cells
    Genome
    Gene Expression

    All Science Journal Classification (ASJC) codes

    • Molecular Biology
    • Genetics
    • Genetics(clinical)

    Cite this

    Okae, H., Hiura, H., Nishida, Y., Funayama, R., Tanaka, S., Chiba, H., ... Arima, T. (2012). Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression. Human Molecular Genetics, 21(3), 548-558. [ddr488]. https://doi.org/10.1093/hmg/ddr488

    Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression. / Okae, Hiroaki; Hiura, Hitoshi; Nishida, Yuichiro; Funayama, Ryo; Tanaka, Satoshi; Chiba, Hatsune; Yaegashi, Nobuo; Nakayama, Keiko; Sasaki, Hiroyuki; Arima, Takahiro.

    In: Human Molecular Genetics, Vol. 21, No. 3, ddr488, 01.02.2012, p. 548-558.

    Research output: Contribution to journalArticle

    Okae, H, Hiura, H, Nishida, Y, Funayama, R, Tanaka, S, Chiba, H, Yaegashi, N, Nakayama, K, Sasaki, H & Arima, T 2012, 'Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression', Human Molecular Genetics, vol. 21, no. 3, ddr488, pp. 548-558. https://doi.org/10.1093/hmg/ddr488
    Okae, Hiroaki ; Hiura, Hitoshi ; Nishida, Yuichiro ; Funayama, Ryo ; Tanaka, Satoshi ; Chiba, Hatsune ; Yaegashi, Nobuo ; Nakayama, Keiko ; Sasaki, Hiroyuki ; Arima, Takahiro. / Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression. In: Human Molecular Genetics. 2012 ; Vol. 21, No. 3. pp. 548-558.
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